Recombinant virus products and methods for inhibition of expression of dux4

ABSTRACT

The present invention relates to RNA interference-based methods for inhibiting the expression of the DUX4 gene, a double homeobox gene on human chromosome 4q35. Recombinant adeno-associated viruses of the invention deliver DNAs encoding microRNAs that knock down the expression of DUX4. The methods have application in the treatment of muscular dystrophies such as facioscapulohumeral muscular dystrophy.

This application claims the benefit of the filing date of U.S.Provisional Patent Application No. 61/511,319 filed Jul. 25, 2011, whichis incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

The present invention relates to RNA interference-based methods forinhibiting the expression of the DUX4 gene, a double homeobox gene onhuman chromosome 4q35. Recombinant adeno-associated viruses of theinvention deliver DNAs encoding microRNAs that knock down the expressionof DUX4. The methods have application in the treatment of musculardystrophies such as facioscapulohumeral muscular dystrophy.

INCORPORATION BY REFERENCE OF THE SEQUENCE LISTING

This application contains, as a separate part of disclosure, a SequenceListing in computer-readable form (filename: 45714PCT_SeqListing.txt;1,661,020 bytes—ASCII text file) which is incorporated by referenceherein in its entirety.

BACKGROUND

Muscular dystrophies (MDs) are a group of genetic diseases. The group ischaracterized by progressive weakness and degeneration of the skeletalmuscles that control movement. Some forms of MD develop in infancy orchildhood, while others may not appear until middle age or later. Thedisorders differ in terms of the distribution and extent of muscleweakness (some forms of MD also affect cardiac muscle), the age ofonset, the rate of progression, and the pattern of inheritance.

Facioscapulohumeral muscular dystrophy (FSHD) is a complex autosomaldominant disorder characterized by progressive and asymmetric weaknessof facial, shoulder and limb muscles. Symptoms typically arise inadulthood with most patients showing clinical features before agethirty. About five percent of patients develop symptoms as infants orjuveniles and these are generally more severely affected. Clinicalpresentation can vary from mild (some limited muscle weakness) to severe(wheelchair dependence). Historically, FSHD was classified as the thirdmost common MD, affecting one in 20,000 individuals worldwide. However,recent data indicate FSHD is the most common MD in Europe, suggestingits worldwide incidence may be underestimated.

Typical FSHD cases (FSHD1A, heretofore referred to as FSHD) are linkedto heterozygous chromosomal deletions that decrease the copy number of3.3 kilobase (kb) D4Z4 repeats on human chromosome 4q35. Simplistically,normal individuals have 11-100 tandemly-repeated D4Z4 copies on both4q35 alleles, while patients with FSHD have one normal and onecontracted allele containing 1-10 repeats. In addition FSHD-associatedD4Z4 contractions must occur on specific disease-permissive chromosome4q35 backgrounds. Importantly, no genes are completely lost orstructurally mutated as a result of FSHD-associated deletions. Thus,although the disease was formally classified in 1954, and the primarygenetic defect identified in 1992, the pathogenic mechanisms remainunresolved.

In leading FSHD pathogenesis models, D4Z4 contractions are proposed tocause epigenic changes that permit expression of genes with myopathicpotential. As a result, aberrant over-expression of otherwise silent ornear-silent genes may ultimately cause MD. This model is consistent withdata showing normal 4q35 D4Z4 repeats have heterochromatincharacteristics, while FSHD-linked D4Z4 repeats contain marks moreindicative of actively transcribed euchromatin. Thesetranscription-permissive epigenetic changes, coupled with theobservation that complete monosomic D4Z4 deletions (i.e., zero repeats)do not cause FSHD, support the hypothesis that D4Z4 repeats harborpotentially myopathic open reading frames (ORFs), which are abnormallyexpressed in FSHD muscles. This notion was initially considered in 1994,when a D4Z4-localized ORF, called DUX4, was first identified. However,the locus had some characteristics of an unexpressed pseudogene and DUX4was therefore summarily dismissed as an FSHD candidate. For many yearsthereafter, the search for FSHD-related genes was mainly focused outsidethe D4Z4 repeats, and although some intriguing candidates emerged fromthese studies, no single gene has been conclusively linked to FSHDdevelopment. This slow progress led to the re-emergence of DUX4 as anFSHD candidate in 2007. Even as of 2010 though, researchers continued tohighlight other genes as candidates. See, for example, Wuebbles et al.,Int. J. Clin. Exp. Pathol., 3(4): 386-400 (2010) highlighting the FSHDregion gene 1 (frg1). In contrast, Wallace et al., Mol. Ther., 17(Suppl.1): S151 (2009); Wei et al., Mol. Ther., 17(Suppl. 1): S200 (2009); andthe Lemmers et al. report from the Sciencexpress issue of Aug. 19, 2010highlight DUX4. Neguembor and Gabellini, Epigenomics, 2(2): 271-287(2010) is a recent review article regarding FSHD.

RNA interference (RNAi) is a mechanism of gene regulation in eukaryoticcells that has been considered for the treatment of various diseases.RNAi refers to post-transcriptional control of gene expression mediatedby microRNAs (miRNAs). The miRNAs are small (21-25 nucleotides),noncoding RNAs that share sequence homology and base-pair with 3′untranslated regions of cognate messenger RNAs (mRNAs). The interactionbetween the miRNAs and mRNAs directs cellular gene silencing machineryto prevent the translation of the mRNAs. The RNAi pathway is summarizedin Duan (Ed.), Section 7.3 of Chapter 7 in Muscle Gene Therapy, SpringerScience+Business Media, LLC (2010).

As an understanding of natural RNAi pathways has developed, researchershave designed artificial miRNAs for use in regulating expression oftarget genes for treating disease. As described in Section 7.4 of Duan,supra, artificial miRNAs can be transcribed from DNA expressioncassettes. The miRNA sequence specific for a target gene is transcribedalong with sequences required to direct processing of the miRNA in acell. Viral vectors such as adeno-associated virus have been used todeliver miRNAs to muscle [Fechner et al., J. Mol. Med., 86: 987-997(2008)].

Adeno-associated virus (AAV) is a replication-deficient parvovirus, thesingle-stranded DNA genome of which is about 4.7 kb in length including145 nucleotide inverted terminal repeat (ITRs). There are multipleserotypes of AAV. The nucleotide sequences of the genomes of the AAVserotypes are known. For example, the complete genome of AAV-1 isprovided in GenBank Accession No. NC_002077; the complete genome ofAAV-2 is provided in GenBank Accession No. NC_001401 and Srivastava etal., J. Virol., 45: 555-564 {1983); the complete genome of AAV-3 isprovided in GenBank Accession No. NC_1829; the complete genome of AAV-4is provided in GenBank Accession No. NC_001829; the AAV-5 genome isprovided in GenBank Accession No. AF085716; the complete genome of AAV-6is provided in GenBank Accession No. NC_00 1862; at least portions ofAAV-7 and AAV-8 genomes are provided in GenBank Accession Nos. AX753246and AX753249, respectively; the AAV-9 genome is provided in Gao et al.,J. Virol., 78: 6381-6388 (2004); the AAV-10 genome is provided in Mol.Ther., 13(1): 67-76 (2006); and the AAV-11 genome is provided inVirology, 330(2): 375-383 (2004). Cis-acting sequences directing viralDNA replication (rep), encapsidation/packaging and host cell chromosomeintegration are contained within the AAV ITRs. Three AAV promoters(named p5, p19, and p40 for their relative map locations) drive theexpression of the two AAV internal open reading frames encoding rep andcap genes. The two rep promoters (p5 and p19), coupled with thedifferential splicing of the single AAV intron (at nucleotides 2107 and2227), result in the production of four rep proteins (rep 78, rep 68,rep 52, and rep 40) from the rep gene. Rep proteins possess multipleenzymatic properties that are ultimately responsible for replicating theviral genome. The cap gene is expressed from the p40 promoter and itencodes the three capsid proteins VP1, VP2, and VP3. Alternativesplicing and non-consensus translational start sites are responsible forthe production of the three related capsid proteins. A single consensuspolyadenylation site is located at map position 95 of the AAV genome.The life cycle and genetics of AAV are reviewed in Muzyczka, CurrentTopics in Microbiology and Immunology, 158: 97-129 (1992).

AAV possesses unique features that make it attractive as a vector fordelivering foreign DNA to cells, for example, in gene therapy. AAVinfection of cells in culture is noncytopathic, and natural infection ofhumans and other animals is silent and asymptomatic. Moreover, AAVinfects many mammalian cells allowing the possibility of targeting manydifferent tissues in vivo. Moreover, AAV transduces slowly dividing andnon-dividing cells, and can persist essentially for the lifetime ofthose cells as a transcriptionally active nuclear episome(extrachromosomal element). The AAV proviral genome is infectious ascloned DNA in plasmids which makes construction of recombinant genomesfeasible. Furthermore, because the signals directing AAV replication,genome encapsidation and integration are contained within the ITRs ofthe AAV genome, some or all of the internal approximately 4.3 kb of thegenome (encoding replication and structural capsid proteins, rep-cap)may be replaced with foreign DNA. The rep and cap proteins may beprovided in trans. Another significant feature of AAV is that it is anextremely stable and hearty virus. It easily withstands the conditionsused to inactivate adenovirus (56° to 65° C. for several hours), makingcold preservation of AAV less critical. AAV may even be lyophilized.Finally, AAV-infected cells are not resistant to superinfection.

There remains a need in the art for a treatment for muscular dystrophiesincluding FSHD.

SUMMARY

The present invention provides methods and products for preventing orinhibiting the expression of the DUX4 gene. The methods of the inventionutilize RNAi to prevent or inhibit the expression of the DUX4 gene. Themethods involve delivering inhibitory RNAs specific for the DUX4 gene tomuscle cells. The DUX4 inhibitory RNAs contemplated include, but are notlimited to, antisense RNAs, small inhibitory RNAs (siRNAs), shorthairpin RNAs (shRNAs) or artificial microRNAs (DUX4 miRNAs) that inhibitexpression of DUX4. Use of the methods and products is indicated, forexample, in preventing or treating FSHD. Some embodiments of theinvention exploit the unique properties of AAV to deliver DNA encodingDUX4 inhibitory RNAs to muscle cells. Other embodiments of the inventionutilize other vectors (for example, other viral vectors such asadenovirus, retrovirus, lentivirus, equine-associated virus, alphavirus,pox viruses, herpes virus, polio virus, sindbis virus and vacciniaviruses) to deliver polynucleotides encoding DUX4 inhibitory RNAs.

In one aspect, the invention provides DUX4 miRNAs. In another aspect,the invention provides rAAV encoding the DUX4 miRNAs wherein the rAAVlack rep and cap genes. In some embodiments, the DUX4 miRNA comprises anmiRNA antisense guide strand selected from those set out in SEQ ID NO:10 through SEQ ID NO: 10912. These sequences comprise antisense “guide”strand sequences of the invention of varying sizes. The antisense guidestrand is the strand of the mature miRNA duplex that becomes the RNAcomponent of the RNA induced silencing complex ultimately responsiblefor sequence-specific gene silencing. See Section 7.3 of Duan, supra.For example, the first antisense guide strand in SEQ ID NO: 10corresponds to (is the reverse complement of) the 3′ end of the DUX4sequence set out in FIG. 1. The second antisense guide strand (SEQ IDNO: 11) is offset one nucleotide from the first and so on. In someembodiments, the GC content of the antisense guide strand is 60% orless, and/or the 5′ end of the antisense guide strand is more AU richwhile the 3′ end is more GC rich. Exemplified DUX4 miRNA are encoded bythe DNAs are set out in SEQ ID NOs: 1 and 2.

In another aspect, the invention provides a composition comprising arAAV encoding a DUX4 miRNA (for example, a rAAV comprising the DNA setout in SEQ ID NO: 1 or 2) wherein the rAAV lacks rep and cap genes.

In yet another aspect, the invention provides a method of preventing orinhibiting expression of the DUX4 gene in a cell comprising contactingthe cell with a rAAV encoding a DUX4 miRNA (for example, a rAAVcomprising the DNA set out in SEQ ID NO: 1 or 2) wherein the rAAV lacksrep and cap genes. Expression of DUX4 may be inhibited by at least 10,20, 30, 40, 50, 60, 70, 80, 90, 95 or 99 percent.

In still another aspect, the invention provides a method of deliveringDNA encoding a DUX4 miRNA to an animal in need thereof, comprisingadministering to the animal a rAAV a DUX4 miRNA (for example, a rAAVcomprising the DNA set out in SEQ ID NO: 1 or 2) wherein the rAAV lacksrep and cap genes.

In yet another aspect, the invention provides a method of preventing ortreating a muscular dystrophy (including, but not limited to, FSHD)comprising administering a rAAV encoding a DUX4 miRNA (for example, arAAV comprising the DNA set out in SEQ ID NO: 1 or 2) wherein the rAAVlacks rep and cap genes. “Treating” includes ameliorating one or moresymptoms of the muscular dystrophy (such as FSHD). Molecular,biochemical, histological and functional endpoints demonstrate thetherapeutic efficacy of DUX4 miRNAs. Endpoints contemplated by theinvention include one or more of: the reduction or elimination of DUX4protein in affected muscles, DUX4 gene knockdown, increase in myofiberdiameters, and improvement in muscle strength.

DETAILED DESCRIPTION

Recombinant AAV genomes of the invention comprise one or more AAV ITRsflanking a polynucleotide encoding, for example, one or more DUX4miRNAs. The polynucleotide is operatively linked to transcriptionalcontrol DNA, specifically promoter DNA that is functional in targetcells. Commercial providers such as Ambion Inc. (Austin, Tex.), DarmaconInc. (Lafayette, Colo.), InvivoGen (San Diego, Calif.), and MolecularResearch Laboratories, LLC (Herndon, Va.) generate custom inhibitory RNAmolecules. In addition, commercially kits are available to producecustom siRNA molecules, such as SILENCER™ siRNA Construction Kit (AmbionInc., Austin, Tex.) or psiRNA System (InvivoGen, San Diego, Calif.).Embodiments include a rAAV genome comprising the DNA set out in SEQ IDNO: 1 encoding the DUX4 miRNA named “miDux4.405” and a rAAV genomecomprising the DNA set out in SEQ ID NO: 2 encoding the DUX4 miRNA named“miDux4.1156.”

The rAAV genomes of the invention lack AAV rep and cap DNA. AAV DNA inthe rAAV genomes may be from any AAV serotype for which a recombinantvirus can be derived including, but not limited to, AAV serotypes AAV-1,AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10 andAAV-11. As noted in the Background section above, the nucleotidesequences of the genomes of various AAV serotypes are known in the art.

DNA plasmids of the invention comprise rAAV genomes of the invention.The DNA plasmids are transferred to cells permissible for infection witha helper virus of AAV (e.g., adenovirus, E1-deleted adenovirus orherpesvirus) for assembly of the rAAV genome into infectious viralparticles. Techniques to produce rAAV particles, in which an AAV genometo be packaged, rep and cap genes, and helper virus functions areprovided to a cell are standard in the art. Production of rAAV requiresthat the following components are present within a single cell (denotedherein as a packaging cell): a rAAV genome, AAV rep and cap genesseparate from (i.e., not in) the rAAV genome, and helper virusfunctions. The AAV rep and cap genes may be from any AAV serotype forwhich recombinant virus can be derived and may be from a different AAVserotype than the rAAV genome ITRs, including, but not limited to, AAVserotypes AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9,AAV-10 and AAV-11. Production of pseudotyped rAAV is disclosed in, forexample, WO 01/83692 which is incorporated by reference herein in itsentirety.

A method of generating a packaging cell is to create a cell line thatstably expresses all the necessary components for AAV particleproduction. For example, a plasmid (or multiple plasmids) comprising arAAV genome lacking AAV rep and cap genes, AAV rep and cap genesseparate from the rAAV genome, and a selectable marker, such as aneomycin resistance gene, are integrated into the genome of a cell. AAVgenomes have been introduced into bacterial plasmids by procedures suchas GC tailing (Samulski et al., 1982, Proc. Natl. Acad. S6. USA,79:2077-2081), addition of synthetic linkers containing restrictionendonuclease cleavage sites (Laughlin et al., 1983, Gene, 23:65-73) orby direct, blunt-end ligation (Senapathy & Carter, 1984, J. Biol. Chem.,259:4661-4666). The packaging cell line is then infected with a helpervirus such as adenovirus. The advantages of this method are that thecells are selectable and are suitable for large-scale production ofrAAV. Other examples of suitable methods employ adenovirus orbaculovirus rather than plasmids to introduce rAAV genomes and/or repand cap genes into packaging cells.

General principles of rAAV production are reviewed in, for example,Carter, 1992, Current Opinions in Biotechnology, 1533-539; and Muzyczka,1992, Curr. Topics in Microbial. and Immunol., 158:97-129). Variousapproaches are described in Ratschin et al., Mol. Cell. Biol. 4:2072(1984); Hermonat et al., Proc. Natl. Acad. Sci. USA, 81:6466 (1984);Tratschin et al., Mol. Cell. Biol. 5:3251 (1985); McLaughlin et al., J.Virol., 62:1963 (1988); and Lebkowski et al., 1988 Mol. Cell. Biol.,7:349 (1988). Samulski et al. (1989, J. Virol., 63:3822-3828); U.S. Pat.No. 5,173,414; WO 95/13365 and corresponding U.S. Pat. No. 5,658,776; WO95/13392; WO 96/17947; PCT/US98/18600; WO 97/09441 (PCT/US96/14423); WO97/08298 (PCT/US96/13872); WO 97/21825 (PCT/US96/20777); WO 97/06243(PCT/FR96/01064); WO 99/11764; Perrin et al. (1995) Vaccine13:1244-1250; Paul et al. (1993) Human Gene Therapy 4:609-615; Clark etal. (1996) Gene Therapy 3:1124-1132; U.S. Pat. Nos. 5,786,211;5,871,982; and 6,258,595. The foregoing documents are herebyincorporated by reference in their entirety herein, with particularemphasis on those sections of the documents relating to rAAV production.

The invention thus provides packaging cells that produce infectiousrAAV. In one embodiment packaging cells may be stably transformed cancercells such as HeLa cells, 293 cells and PerC.6 cells (a cognate 293line). In another embodiment, packaging cells are cells that are nottransformed cancer cells, such as low passage 293 cells (human fetalkidney cells transformed with E1 of adenovirus), MRC-5 cells (humanfetal fibroblasts), WI-38 cells (human fetal fibroblasts), Vero cells(monkey kidney cells) and FRhL-2 cells (rhesus fetal lung cells).

Recombinant AAV (i.e., infectious encapsidated rAAV particles) of theinvention comprise a rAAV genome. Embodiments include, but are notlimited to, the rAAV named “AAV.miDUX4.405” including a genome encodingthe DUX4 miRNA hDux.mi405 (encoded by the DNA set out in SEQ ID NO: 1and the rAAV named “AAV.miDUX4.1156” including a genome encoding theDUX4 miRNA hDux.mi1156 (encoded by the DNA set out in SEQ ID NO: 2). Thegenomes of both rAAV lack AAV rep and cap DNA, that is, there is no AAVrep or cap DNA between the ITRs of the genomes.

The rAAV may be purified by methods standard in the art such as bycolumn chromatography or cesium chloride gradients. Methods forpurifying rAAV vectors from helper virus are known in the art andinclude methods disclosed in, for example, Clark et al., Hum. GeneTher., 10(6): 1031-1039 (1999); Schenpp and Clark, Methods Mol. Med., 69427-443 (2002); U.S. Pat. No. 6,566,118 and WO 98/09657.

In another embodiment, the invention contemplates compositionscomprising rAAV of the present invention. Compositions of the inventioncomprise rAAV in a pharmaceutically acceptable carrier. The compositionsmay also comprise other ingredients such as diluents and adjuvants.Acceptable carriers, diluents and adjuvants are nontoxic to recipientsand are preferably inert at the dosages and concentrations employed, andinclude buffers such as phosphate, citrate, or other organic acids;antioxidants such as ascorbic acid; low molecular weight polypeptides;proteins, such as serum albumin, gelatin, or immunoglobulins;hydrophilic polymers such as polyvinylpyrrolidone; amino acids such asglycine, glutamine, asparagine, arginine or lysine; monosaccharides,disaccharides, and other carbohydrates including glucose, mannose, ordextrins; chelating agents such as EDTA; sugar alcohols such as mannitolor sorbitol; salt-forming counterions such as sodium; and/or nonionicsurfactants such as Tween, pluronics or polyethylene glycol (PEG).

Titers of rAAV to be administered in methods of the invention will varydepending, for example, on the particular rAAV, the mode ofadministration, the treatment goal, the individual, and the cell type(s)being targeted, and may be determined by methods standard in the art.Titers of rAAV may range from about 1×10⁶, about 1×10⁷, about 1×10⁸,about 1×10⁹, about 1×10¹⁰, about 1×10¹¹, about 1×10¹², about 1×10¹³ toabout 1×10¹⁴ or more DNase resistant particles (DRP) per ml. Dosages mayalso be expressed in units of viral genomes (vg).

Methods of transducing a target cell with rAAV, in vivo or in vitro, arecontemplated by the invention. The in vivo methods comprise the step ofadministering an effective dose, or effective multiple doses, of acomposition comprising a rAAV of the invention to an animal (including ahuman being) in need thereof. If the dose is administered prior todevelopment of a disorder/disease, the administration is prophylactic.If the dose is administered after the development of a disorder/disease,the administration is therapeutic. In embodiments of the invention, aneffective dose is a dose that alleviates (eliminates or reduces) atleast one symptom associated with the disorder/disease state beingtreated, that slows or prevents progression to a disorder/disease state,that slows or prevents progression of a disorder/disease state, thatdiminishes the extent of disease, that results in remission (partial ortotal) of disease, and/or that prolongs survival. An example of adisease contemplated for prevention or treatment with methods of theinvention is FSHD.

Combination therapies are also contemplated by the invention.Combination as used herein includes both simultaneous treatment orsequential treatments. Combinations of methods of the invention withstandard medical treatments (e.g., corticosteroids) are specificallycontemplated, as are combinations with novel therapies.

Administration of an effective dose of the compositions may be by routesstandard in the art including, but not limited to, intramuscular,parenteral, intravenous, oral, buccal, nasal, pulmonary, intracranial,intraosseous, intraocular, rectal, or vaginal. Route(s) ofadministration and serotype(s) of AAV components of the rAAV (inparticular, the AAV ITRs and capsid protein) of the invention may bechosen and/or matched by those skilled in the art taking into accountthe infection and/or disease state being treated and the targetcells/tissue(s) that are to express the DUX4 miRNAs.

In particular, actual administration of rAAV of the present inventionmay be accomplished by using any physical method that will transport therAAV recombinant vector into the target tissue of an animal.Administration according to the invention includes, but is not limitedto, injection into muscle, the bloodstream and/or directly into theliver. Simply resuspending a rAAV in phosphate buffered saline has beendemonstrated to be sufficient to provide a vehicle useful for muscletissue expression, and there are no known restrictions on the carriersor other components that can be co-administered with the rAAV (althoughcompositions that degrade DNA should be avoided in the normal mannerwith rAAV). Capsid proteins of a rAAV may be modified so that the rAAVis targeted to a particular target tissue of interest such as muscle.See, for example, WO 02/053703, the disclosure of which is incorporatedby reference herein. Pharmaceutical compositions can be prepared asinjectable formulations or as topical formulations to be delivered tothe muscles by transdermal transport. Numerous formulations for bothintramuscular injection and transdermal transport have been previouslydeveloped and can be used in the practice of the invention. The rAAV canbe used with any pharmaceutically acceptable carrier for ease ofadministration and handling.

For purposes of intramuscular injection, solutions in an adjuvant suchas sesame or peanut oil or in aqueous propylene glycol can be employed,as well as sterile aqueous solutions. Such aqueous solutions can bebuffered, if desired, and the liquid diluent first rendered isotonicwith saline or glucose. Solutions of rAAV as a free acid (DNA containsacidic phosphate groups) or a pharmacologically acceptable salt can beprepared in water suitably mixed with a surfactant such ashydroxypropylcellulose. A dispersion of rAAV can also be prepared inglycerol, liquid polyethylene glycols and mixtures thereof and in oils.Under ordinary conditions of storage and use, these preparations containa preservative to prevent the growth of microorganisms. In thisconnection, the sterile aqueous media employed are all readilyobtainable by standard techniques well-known to those skilled in theart.

The pharmaceutical forms suitable for injectable use include sterileaqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersions. In all cases the form must be sterile and must be fluid tothe extent that easy syringability exists. It must be stable under theconditions of manufacture and storage and must be preserved against thecontaminating actions of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, liquidpolyethylene glycol and the like), suitable mixtures thereof, andvegetable oils. The proper fluidity can be maintained, for example, bythe use of a coating such as lecithin, by the maintenance of therequired particle size in the case of a dispersion and by the use ofsurfactants. The prevention of the action of microorganisms can bebrought about by various antibacterial and antifungal agents, forexample, parabens, chlorobutanol, phenol, sorbic acid, thimerosal andthe like. In many cases it will be preferable to include isotonicagents, for example, sugars or sodium chloride. Prolonged absorption ofthe injectable compositions can be brought about by use of agentsdelaying absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating rAAV in therequired amount in the appropriate solvent with various otheringredients enumerated above, as required, followed by filtersterilization. Generally, dispersions are prepared by incorporating thesterilized active ingredient into a sterile vehicle which contains thebasic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, the preferred methods of preparation arevacuum drying and the freeze drying technique that yield a powder of theactive ingredient plus any additional desired ingredient from thepreviously sterile-filtered solution thereof.

Transduction with rAAV may also be carried out in vitro. In oneembodiment, desired target muscle cells are removed from the subject,transduced with rAAV and reintroduced into the subject. Alternatively,syngeneic or xenogeneic muscle cells can be used where those cells willnot generate an inappropriate immune response in the subject.

Suitable methods for the transduction and reintroduction of transducedcells into a subject are known in the art. In one embodiment, cells canbe transduced in vitro by combining rAAV with muscle cells, e.g., inappropriate media, and screening for those cells harboring the DNA ofinterest using conventional techniques such as Southern blots and/orPCR, or by using selectable markers. Transduced cells can then beformulated into pharmaceutical compositions, and the compositionintroduced into the subject by various techniques, such as byintramuscular, intravenous, subcutaneous and intraperitoneal injection,or by injection into smooth and cardiac muscle, using e.g., a catheter.

Transduction of cells with rAAV of the invention results in sustainedexpression of DUX4 miRNAs. The present invention thus provides methodsof administering/delivering rAAV which express DUX4 miRNAs to an animal,preferably a human being. These methods include transducing tissues(including, but not limited to, tissues such as muscle, organs such asliver and brain, and glands such as salivary glands) with one or morerAAV of the present invention. Transduction may be carried out with genecassettes comprising tissue specific control elements. For example, oneembodiment of the invention provides methods of transducing muscle cellsand muscle tissues directed by muscle specific control elements,including, but not limited to, those derived from the actin and myosingene families, such as from the myoD gene family [See Weintraub et al.,Science, 251: 761-766 (1991)], the myocyte-specific enhancer bindingfactor MEF-2 [Cserjesi and Olson, Mol Cell Biol 11: 4854-4862 (1991)],control elements derived from the human skeletal actin gene [Muscat etal., Mol Cell Biol, 7: 4089-4099 (1987)], the cardiac actin gene, musclecreatine kinase sequence elements [See Johnson et al., Mol Cell Biol,9:3393-3399 (1989)] and the murine creatine kinase enhancer (mCK)element, control elements derived from the skeletal fast-twitch troponinC gene, the slow-twitch cardiac troponin C gene and the slow-twitchtroponin I gene: hypoxia-inducible nuclear factors [Semenza et al., ProcNatl Acad Sci USA, 88: 5680-5684 (1991)], steroid-inducible elements andpromoters including the glucocorticoid response element (GRE) [See Maderand White, Proc. Natl. Acad. Sci. USA 90: 5603-5607 (1993)], and othercontrol elements.

Muscle tissue is an attractive target for in vivo DNA delivery, becauseit is not a vital organ and is easy to access. The inventioncontemplates sustained expression of miRNAs from transduced myofibers.

By “muscle cell” or “muscle tissue” is meant a cell or group of cellsderived from muscle of any kind (for example, skeletal muscle and smoothmuscle, e.g. from the digestive tract, urinary bladder, blood vessels orcardiac tissue). Such muscle cells may be differentiated orundifferentiated, such as myoblasts, myocytes, myotubes, cardiomyocytesand cardiomyoblasts.

The term “transduction” is used to refer to the administration/deliveryof DUX4 miRNAs to a recipient cell either in vivo or in vitro, via areplication-deficient rAAV of the invention resulting in expression of aDUX4 miRNA by the recipient cell.

Thus, the invention provides methods of administering an effective dose(or doses, administered essentially simultaneously or doses given atintervals) of rAAV that encode DUX4 miRNAs to a patient in need thereof.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows the human DUX4 DNA sequence.

FIGS. 2A and 2B set out sequences of DUX4 targeted miRNAs. In eachpanel, the top sequences indicate the DNA templates from which eachrespective miRNA is transcribed. In the top panel, the DNA templatemiDUX4.405 is SEQ ID NO: 1. In the bottom panel, the DNA templatemiDUX4.1156 is SEQ ID NO: 2. The folded miRNA transcripts are shown ashairpin structures. The miDUX4.405 folded miRNA is SEQ ID NO: 8. ThemiDUX4.1156 folded miRNA is SEQ ID NO: 9. The mature miDUX4.405 andmiDUX4.1156 sequences arise following processing in target cells by hostmiRNA processing machinery (including Drosha, DGCR8, Dicer, andExportin-5). Sequences shaded in gray indicate restriction sites usedfor cloning each miRNA into the U6T6 vector. CTCGAG is an XhoI site andACTAGT is a SpeI site (CUCGAG and ACUAGU in RNA, where the U is a uracilbase). The red sequence indicates the mature miRNA antisense guidestrand that ultimately helps catalyze cleavage of the DUX4 target mRNA.This sequence is also underlined in the miRNA hairpin portions of thisdiagram. The gray and black arrowheads indicate Drosha- andDicer-catalyzed cleavage sites, respectively. The numbers 13, 35, 53,and 75 are provided for orientation. The sequences between (andincluding) positions 35-53 are derived from the natural human mir-30asequence, except the A at position 39, which is a G is the normalmir-30a sequence. We changed this nucleotide to an A to facilitatefolding of the miRNA loop, based on in silico RNA folding models. Thebase of the stem (5′ of position 13 and 3′ of position 75) is alsoderived from mir-30a structure and sequence with some modificationsdepending on the primary sequence of the guide strand. Specifically, thenucleotide at position 13 can vary to help facilitate a requiredmismatched between the position 13 and 75 nucleotides. This bulgedstructure is hypothesized to facilitate proper Drosha cleavage.

FIGS. 3A and 3B relate to a luciferase assay used for initial miDUX4efficacy screens. FIG. 3A shows the dual luciferase reporter plasmidused for in vitro screens. This vector is modified from a commerciallyavailable plasmid (psiCheck2) obtained from Promega. The human DUX4 cDNAwas cloned downstream of the Renilla luciferase gene, as shown. Thisconformation does not produce a Luciferase—DUX4 fusion protein, sincethe DUX4 sequences are placed after the Renilla luciferase stop codon.Instead, a fusion mRNA is produced, in which the DUX4 sequences are thede facto 3′ untranslated region (3′ UTR) of Renilla luciferase. As aresult, any effective DUX4-targeted miRNA will reduce the RenillaLuciferase-DUX4 fusion mRNA, which subsequently decreases Renillaluciferase protein expression in transfected cells. There is a separateFirefly luciferase gene located on the same plasmid, which does notcontain any DUX4 sequences and is therefore unaffected by DUX4-targetedmiRNAs. FIG. 3B shows Firefly and Renilla luciferase activity quantifiedseparately in cells using a Dual Luciferase Assay Kit (Promega). DUX4gene silencing is therefore measured indirectly and indicated by a lowratio of Renilla:Firefly luciferase activity. All samples in this assayare normalized to cells co-transfected with our reporter vector and theU6.miGFP control miRNA. Samples transfected with miDUX4.405 andmiDUX4.1156 had consistently lower Renilla luciferase activity,indicating DUX4 gene silencing. Data in B are representative of twoindependent experiments performed on different days in triplicate. Errorbars indicate standard error of the mean (s.e.m.).

FIG. 4A is a diagram of constructs used in Western blot experimentsshowing AAV.miDUX4 proviral plasmids reduce DUX4 protein expression invitro. In the diagram of the constructs, the black rectangles indicateAAV inverted terminal repeats (ITRs), CMV is the cytomegaloviruspromoter, hrGFP is a green fluorescent protein coding region, pA is theSV40 polyA signal and V5 refers to the V5 epitope which was inserted inframe at the C terminus of human DUX4 to facilitate detection withcommercially available V5 epitope antibodies (Invitrogen). The U6.miDUX4sequences (405 and 1156) and U6.miGFP control were cloned upstream ofthe CMV.hrGFP.pA cassette, as shown. Proviral plasmids wereco-transfected into HEK293 cells with the CMV.DUX4.V5 expression vectorshown at the top of FIG. 4A. FIG. 4B shows Western blots usingantibodies targeting the V5 epitope (DUX4) demonstrating DUX4 genesilencing by both miDUX4 sequences, compared to the non-targeting miGFPcontrol. GAPDH antibodies were used to control for equivalent loading ofprotein extracts for the experiment. The ‘Unt’ lane contains proteinextracts from untransfected HEK293 cells.

FIG. 5 is a diagram of genomes of rAAV encoding DUX4 miRNAs.

EXAMPLES

The role of DUX4 in FSHD pathogenesis can be explained as follows.First, D4Z4 repeats are not pseudogenes. The DUX4 locus produces 1.7 kband 2.0 kb full-length mRNAs with identical coding regions, and D4Z4repeats also harbor smaller sense and antisense transcripts, includingsome resembling microRNAs. Over-expressed DUX4 transcripts and a ˜50 kDafull-length DUX4 protein are found in biopsies and cell lines from FSHDpatients. These data are consistent with a transcriptional de-repressionmodel of FSHD pathogenesis. In addition, unlike pseudogenes, D4Z4repeats and DUX4 likely have functional importance, sincetandemly-arrayed D4Z4 repeats are conserved in at least eleven differentplacental mammalian species (non-placental animals lack D4Z4 repeats),with the greatest sequence conservation occurring within the DUX4 ORF.Second, over-expressed DUX4 is toxic to tissue culture cells andembryonic progenitors of developing lower organisms in vivo. Thistoxicity occurs at least partly through a pro-apoptotic mechanism,indicated by Caspase-3 activation in DUX4 transfected cells, andpresence of TUNEL-positive nuclei in developmentally arrested Xenopusembryos injected with DUX4 mRNA at the two-cell stage. These findingsare consistent with studies showing some pro-apoptotic proteins,including Caspase-3, are present in FSHD patient muscles. In addition tostimulating apoptosis, DUX4 may negatively regulate myogenesis. HumanDUX4 inhibits differentiation of mouse C2C12 myoblasts in vitro,potentially by interfering with PAX3 and/or PAX7, and causesdevelopmental arrest and reduced staining of some muscle markers whendelivered to progenitor cells of zebrafish or Xenopus embryos. Finally,aberrant DUX4 function is directly associated with potentially importantmolecular changes seen in FSHD patient muscles. Specifically,full-length human DUX4 encodes an approximately 50 kDa doublehomeodomain transcription factor, and its only known target, Pitx1, waselevated in DUX4 over-expressing FSHD patient muscles. These datasupport that DUX4 catalyzes numerous downstream molecular changes thatare incompatible with maintaining normal muscle integrity.

Thus, aspects and embodiments of the invention are illustrated by thefollowing examples. Example 1 describes miRNAs specific for the DUX4gene. Example 2 describes the effect of the miRNAs on the expression ofDUX4 as measured by luciferase assay. Example 3 describes the in vitroeffect of proviral plasmids expressing the miRNAs on the expression ofDUX4 as measured by Western blot. Example 4 describes rAAV vectorsencoding DUX4 miRNAs. Example 5 describes mitigation of DUX4-inducedmyopathy by AAV6.miDUX4.405 vectors. Example 6 describes protection ofmuscles from pathological muscles changes associated with FSHD. Example7 describes the protection of mice from DUX4-associated grip strengthdeficits.

Example 1 MicroRNAs Specific for the DUX4 Gene

Two miRNAs specific for the DUX4 gene were generated by PCR. Four PCRprimers were used that had the following sequences.

Primer 662 (miDUX4hum405F): (SEQ ID NO: 3)AAAACTCGAGTGAGCGATCCAGGATTCAGATCTGGTTTCTGAAAGC CACAGATGGGPrimer 663 (miDUX4hum405R): (SEQ ID NO: 4)TTTTACTAGTAGGCAGTCCAGGATTCAGATCTGGTTTCCCATCTGT GGCTTTCAGPrimer 665 (miDUX4hum1156F): (SEQ ID NO: 5)AAAACTCGAGTGAGCGAAGGCGCAACCTCTCCTAGAAACTGAAAGC CACAGATGGGPrimer 667 (miDUX4hum1156R): (SEQ ID NO: 6)TTTTACTAGTAGGCACAGGCGCAACCTCTCCTAGAAACCCATCTGT GGCTTTCAG

DNA encoding a miRNA designated hDux.mi405 was generated using primers662 and 663. DNA encoding miRNA designated hDux.mi1156 was generatedusing primers 665 and 667.

One μg of each primer was added to a 1 cycle primer extension reaction:95° C. for 5 min.; 94° C. for 2 min.; 52° C. for 1 min.; 72° C. for 15min.; and then holding at 4° C. The PCR products were cleaned up withthe Qiagen QIAquick PCR Purification kit before being digested overnightwith XHOI and SPEI restriction enzymes. The digestion product was thenrun on a 1.5% TBE gel and the band excised and purified using the QiagenQIAquick Gel Extraction Kit. The sequences of the miRNAs are set outbelow and in FIGS. 2A and 2B, respectively.

miDux4.405 (SEQ ID NO: 1) CTCGAGTGAGCGATCCAGGATTCAGATCTGGTTTCTGAAAGCCACAGATGGGAAACCAGATCTGAATCCTGGACTGCCTACTAGT miDux4.1156 (SEQ ID NO: 2)CTCGAGTGAGCGAAGGCGCAACCTCTCCTAGAAACTGAAAGCCACAGATGGGTTTCTAGGAGAGGTTGCGCCTGTGCCTACTAGT

The two PCR products were ligated overnight to a U6T6 vector (via XhoIand XbaI) that contains a mouse U6 promoter and an RNA polymerase IIItermination signal (six thymidine nucleotides). MiRNAs are cloned intoXhoI and XbaI restriction sites located between the 3′ end of the U6promoter and termination signal (SpeI site on the 3′ end of the DNAtemplate for each miRNA has complementary cohesive ends with the XbaIsite). The ligation product was transformed into chemically competentE-coli cells with a 42° C. heat shock and incubated at 37° C. shakingfor 1 hour before being plated on kanamycin selection plates. Thecolonies were allowed to grow overnight at 37°. The following day theywere mini-prepped and sequenced for accuracy.

Example 2 Luciferase Assay for Effect of Expression of DUX4 miRNAs

Expression of the DUX4 target sequence in the presence of the DUX4miRNAs was assayed. A lipofectamine 2000 transfection was done in 293cells in a 96-well, white-walled assay plate. 140,000 cells weretransfected with 20 ng of a Renilla-firefly plasmid containing the DUX4target sequence (FIG. 3A) and 180 ng of various DUX4 miRNA-encodingvectors, including U6T6-driven miDux4.405 or miDux4.1156 vectors fromExample 1. A luciferase assay was performed 24 hours later.

The media was removed from the cells and 20 μl of lysis buffer was addedper well. The plate was put on a shaker for 15 minutes at roomtemperature before adding 50 μl of luciferase substrate. The firstreading was taken 10 minutes later. Next, 50 μl of Stop and Gloluciferase substrate was added and the second reading was taken 10minutes later. The Renilla expression was divided by the fireflyexpression to calculate the relative expression. The relative expressionwas then normalized to the expression of cells that were transfectedwith a control miRNA that targets eGFP. Results are shown in FIG. 3B.The DUX4 miRNAs miDUX4.405 and miDUX4.1156 were the most effective atreducing luciferase protein expression in transfected cells.

Example 3 Western Blot Assay for Effect of Expression of DUX4 miRNAsfrom rAAV

Next, the U6T6.miDUX4 miRNA expression cassettes were cloned intoAAV.CMV.hrGFP proviral plasmids as shown in the FIG. 4A. The proviralplasmids were then co-transfected with a DUX4.V5 expression plasmid into293 cells and the effect of expression of DUX4 miRNAs from the proviralplasmids was assayed by Western blot. A U6.miGFP sequence, which doesnot target DUX4, was used as a negative control for gene silencing.

One day before transfection, 293 cells were plated in a 24-well plate at1.5×10⁵ cells/well. The cells were then transfected with AAV-CMV-DUX4-V5and AAV-CMV-miDUX4 (405 or 1156) using Lipofectamine 2000 (Invitrogen,Cat. No. 11668-019):

Group 1: AAV-CMV-DUX4-V5 50 ng+AAV-CMV-miDUX4 800 ng (1:16)Group 2: AAV-CMV-DUX4-V5 100 ng+AAV-CMV-miDUX4 800 ng (1:8)

Thirty-six h after transfection, cells were collected and washed withcold PBS once. Seventy μl lysis buffer (137 mM NaCl, 10 mM Tris pH=7.4,1% NP40) were then added. The cells were resuspended completely andincubated on ice for 30 min. The samples were centrifuged for 20 min at13,000 rpm at 4° C. and the supernatant was collected. The cell lysatewas diluted 5-fold for the Lowry protein concentration assay (Bio-Rad DcProtein Assay Reagent A, B, S; Cat. No. 500-0113, 500-0114, 500-115).Twenty-three μg of each sample was taken and 2× sample buffer (100 mMTris pH=6.8, 100 mM DTT, 10% glycerol, 2% SDS, 0.006% bromophenol blue)was added. The samples were boiled for 10 min and then put on ice.

The samples were loaded onto 10% polyacrylamide gels (based on 37.5:1acrylamide:bis acrylamide ratio, Bio-Rad, Cat. No. 161-0158), 3.5 μg and18 μg on two gels for each sample. Proteins were transferred to PVDFmembranes at 15 V for 1 h using semi-dry transfer (Trans-Blot SDSemi-Dry Transfer Cell, Bio-Rad, Cat. No. 170-3940). The blots wereplaced into blocking buffer (5% non-fat dry milk, 30 mM Tris pH=7.5, 150mM NaCl, 0.05% Tween-20) and agitated for 1 h at room temperature. Theblocking buffer was decanted and anti-DUX4 primary antibody solution(DUX4 p12, Santa Cruz, Cat. No. sc-79927, 1:1,000) was added andincubated with agitation overnight at 4° C. The membranes were thenwashed for 30 min, changing the wash buffer (150 mM NaCl, 30 mM TrispH=7.5, 0.05% Tween-20) every 10 min. Peroxidase-conjugated DonkeyAnti-Goat Antibody (Jackson ImmunoReserch, Cat. No. 705-035-003, 1:100,000) was added and incubated at room temperature for 2 h. Themembranes were then washed for 30 min, changing the wash buffer every 10min. The blots were placed in chemiluminescent working solution(Immobilon Western Chemiluminescent HRP Substrate, Millipore, Cat. No.WBKLS0500), incubated with agitation for 5 min at room temperature, andthen exposed to X-ray film.

The membranes were washed for 20 min, changing the wash buffer every 10min. Next, stripping buffer (2% SDS, 62.5 mM Tris pH=6.7, 100 mM b-ME)was added to the blots and incubated at 50° C. for 30 min. The membraneswere washed again for 30 min, changing the wash buffer every 10 min.Then, the membranes were blocked again and re-probed with Anti-GAPDHprimary antibody solution (Chemicon, Cat. No. MAB374, 1:200) andperoxidase-conjugated Goat Anti-Mouse Antibody (Jackson ImmunoReserch,Cat. No. 115-035-146, 1:100,000) was used as secondary antibody.

Finally, the membranes were stripped again and re-probed with anti-V5antibody (Invitrogen, Cat. No. R960-25, 1:5,000).

The AAV.miDUX4 proviral plasmids reduced DUX4 protein expression invitro. AAV-CMV-miDUX4.405 was the most effective at knocking down DUX4expression.

Example 4 Production of rAAV Encoding DUX4 MicroRNAs

Vector was produced by co-transfection in HEK293 cells of three plasmids(pAdhelper, AAV helper, and the rAAV genome containing miDUX4; describedin detail below), followed by cell-harvesting, vector purification,titration, and quality control assays.

Plasmids:

pAdhelper contains the adenovirus genes E2A, E4 ORF6, and VA I/II; AAVhelper plasmids contain AAV rep2 and cap6 (for example, for an AAVserotype 6 preparation, the capsid gene would be called cap6); the rAAVplasmid contains AAV inverted terminal repeat (ITRs) sequences flankingthe genetic elements to be packaged into the vector. For the AAV.miDUX4,this includes the U6.miDUX4 cloned upstream of the CMV.eGFP reportergene.

Transfection:

Plasmids were transfected into 293 cells (Corning 10-Stack) using CaPO₄at a 4:4:1 ratio (20 ug pAd helper: 20 ug AAV helper: 5 ug rAAV vectorplasmid per plate.

Cell Harvesting:

Forty-eight hr post-transfection, cells were harvested and resuspendedin 20 mM Tris (pH 8.0), 1 mM MgCl₂ and 150 mM NaCl (T20M1N150) at adensity of 5×10⁶ cells/ml. Cells were lysed by four sequentialfreeze/thaw cycles and Benzonase nuclease (AIC, Stock: 250 U/ul) addedto a final concentration of 90 U/ml before cell lysate clarification.

Vector Purification and Titration:

Clarified lysates were subjected to iodixanol step gradient purificationas previously described (Xiao, X, et al. J. Virol 72:2224-32). The 40%iodixanol layer (containing rAAV) was diluted 5-fold with a no-saltdilution buffer (pH varying depending on serotype) and applied to aHi-Trap HP-Q/S column. Upon elution with a NaCl salt gradient, peak 1 mlfractions (typically 3-5) were pooled, dialyzed with T20M1N200 (pH 8.0),then sterile filtered and supplemented with 0.001% Pluronic F68. Vectorwas stored at −80° C. Purified virus was titered for vg using Q-PCR aspreviously described [Schnepp and Clark, Methods Mol. Med., 69:427-443(2002)].

Schematic diagrams of the rAAV genomes are shown in FIG. 5.

Example 5 AAV6.miDUX4s Mitigated DUX4-Associated Muscle Toxicity In Vivo

Adult wild-type male C57BL/6 mice were co-injected with 1) 3×10⁹ DNaseresistant particles (DRP) of AAV.CMV.DUX4.V5 or were sham injected, and2) 3×10¹⁰ DRP of AAV.miDUX4 or control AAV.CMV.GFP into the tibialisanterior muscle. Animals were sacrificed two weeks later. Muscles werecryopreserved and cut into 10 mm cryosections, then stained withhematoxylin and erosion (H&E).

Animals that received DUX4 and eGFP vectors showed histologicalindicators of muscle damage. Specifically, these muscle sectionscontained abundant myofibers with centrally-located nuclei, small-boremyofibers (both of which indicate newly regenerated muscle), anddeposition of fibrotic tissue. At 4 weeks, miDUX4-treated animals wereindistinguishable from sham-injected normal wild-type muscles.

MiDUX4-treatment significantly mitigated DUX4-induced muscledegeneration, compared to control GFP-injected muscles.

Example 6 AAV6.miDUX4s Protected Muscles from Pathological MolecularChanges Associated with FSHD

Caspase-3 is expressed in myofibers of FSHD patients and is activated byDUX4 expression in mouse muscle. The effect of expression of DUX4 in thepresence and absence of AAV6.miDUX4 was examined.

Eight-week-old C57BL/6 female mice received 50 μl direct intramuscularinjections into the tibialis anterior. Premixed virus cocktailscontained 8×10⁸ DNAse resistant particles of AAV6.DUX4 and 3×10¹⁰ ofeither AAV6.miDUX4 or AAV6.eGFP. Muscle samples were prepared asdescribed in Example 5 and stained with cleaved Caspase-3 (CellSignaling Technology, Danvers, Mass.) polyclonal antibodies by standardmethods.

Uninhibited DUX4 expression was associated with caspase-3 positivelesions in AAV6.DUX4-transduced control muscles in mice. In contrast,there were no caspase-3 positive myofibers in muscles coinjected withAAV6.DUX4 and AAV.miDUX4 vectors.

Example 7 AAV6.miDUX4s Protect Mice from DUX4-Associated Grip StrengthDeficits

The effects of AAV6.miDUX4 on DUX4-associated hindlimb grip strengthdeficits in mice were measured.

Grip strength was measured in forelimbs and hindlimbs of C57BL/6 mice(n=8 animals) one week before injection to establish a baseline, andthen weekly up to 4 weeks postinjection as previously described inWallace et al., Ann. Neurol., 69: 540-552 (2011). By two weeks, miceinjected with AAV6.DUX4 alone or AAV6.DUX4 with control AAV.eGFP showedsignificantly reduced grip strength compared to all other groups. Thistimepoint is consistent with the onset of degeneration in musclecryosections. Weakness resolved in three weeks, as regenerativeprocesses were underway. In contrast, animals coinjected with AAV6.DUX4and AAV6.miDUX4 were not significantly weaker than saline-injected wildtype mice at any timepoint following injection. Mice that receivedAAV6.miDUX4 alone were unaffected, indicating miDUX4 expression waswell-tolerated by normal muscles.

While the present invention has been described in terms of specificembodiments, it is understood that variations and modifications willoccur to those skilled in the art. Accordingly, only such limitations asappear in the claims should be placed on the invention.

All documents referred to in this application are hereby incorporated byreference in their entirety.

1-12. (canceled)
 13. A method of inhibiting expression of the DUX4 genein a cell comprising contacting the cell with a recombinantadeno-associated virus comprising a DNA encoding a DUX4 miRNA comprisingan miRNA antisense guide strand, wherein the miRNA antisense guidestrand consists of the nucleotide sequence of SEQ ID NO: 8482, SEQ IDNO: 8372, SEQ ID NO: 8371, SEQ ID NO: 8370, SEQ ID NO: 8367, SEQ ID NO:8366, SEQ ID NO: 8365, SEQ ID NO: 8219, SEQ ID NO: 8218, SEQ ID NO:8152, SEQ ID NO: 8147, SEQ ID NO: 8145, SEQ ID NO: 7397, SEQ ID NO:7396, SEQ ID NO: 7395, SEQ ID NO: 7108, SEQ ID NO: 7107, SEQ ID NO:7106, SEQ ID NO: 6633, SEQ ID NO: 6631, SEQ ID NO: 6622, SEQ ID NO:6619, SEQ ID NO: 6609, SEQ ID NO: 6608, SEQ ID NO: 6568, SEQ ID NO: 6561or SEQ ID NO:
 6560. 14. A method of treating a subject suffering from afacioscapulohumeral muscular dystrophy comprising administering to thesubject a recombinant adeno-associated virus comprising a DNA encoding aDUX4 miRNA comprising an miRNA antisense guide strand, wherein the miRNAantisense guide strand consists of the nucleotide sequence of SEQ ID NO:8482, SEQ ID NO: 8372, SEQ ID NO: 8371, SEQ ID NO: 8370, SEQ ID NO:8367, SEQ ID NO: 8366, SEQ ID NO: 8365, SEQ ID NO: 8219, SEQ ID NO:8218, SEQ ID NO: 8152, SEQ ID NO: 8147, SEQ ID NO: 8145, SEQ ID NO:7397, SEQ ID NO: 7396, SEQ ID NO: 7395, SEQ ID NO: 7108, SEQ ID NO:7107, SEQ ID NO: 7106, SEQ ID NO: 6633, SEQ ID NO: 6631, SEQ ID NO:6622, SEQ ID NO: 6619, SEQ ID NO: 6609, SEQ ID NO: 6608, SEQ ID NO:6568, SEQ ID NO: 6561 or SEQ ID NO:
 6560. 15. The method of claim 13,wherein the recombinant adeno-associated virus lacks rep and cap genes.16. The method of claim 14, wherein the recombinant adeno-associatedvirus lacks rep and cap genes.
 17. The method of claim 14, wherein theadministering comprises injecting into the muscle, the bloodstream, orthe liver, or a target tissue of the subject.